Quick Guides

Quick guides to obtain necessary data — methodology, installation, commands, and detailed chart descriptions for every tool integrated in IntMeta.

Taxonomic Classification

3 tools

31 charts

Kraken2

Kraken2 is an ultrafast k-mer based taxonomic sequence classifier that assigns taxonomic labels to short DNA reads by examining the k-mers within a read and querying a database with those k-mers.

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30 charts

CLARK

CLARK (CLAssifier based on Reduced K-mers) is a supervised sequence classification method that uses discriminative k-mers — k-mers unique to a specific taxon — for fast and precise metagenomic classification.

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30 charts

Kaiju

Kaiju is a protein-level metagenomic classifier that translates DNA reads into amino acid sequences and matches them against a reference protein database using the Burrows-Wheeler transform (BWT).

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Metagenomic Binning

4 tools

32 charts

CheckM2

CheckM2 is a rapid machine-learning-based tool for assessing the quality of metagenome-assembled genomes (MAGs). It uses gradient-boosted models trained on genomic features to predict completeness and contamination without requiring reference genomes.

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30 charts

DAS Tool

DAS Tool is an automated method for optimizing metagenome-assembled genome (MAG) recovery by integrating the results of multiple binning algorithms. It selects the best non-redundant set of bins from several input binners using single-copy gene (SCG) analysis.

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22 charts

VAMB

VAMB (Variational Autoencoders for Metagenomic Binning) uses deep variational autoencoders to learn a latent representation of contigs from their tetranucleotide frequencies and co-abundance profiles across multiple samples, enabling accurate metagenomic binning.

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22 charts

SemiBin2

SemiBin2 is a self-supervised deep learning method for metagenomic binning. It uses contrastive learning with data augmentation to train sample-specific models without requiring reference genomes, enabling accurate binning even for novel environments.

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Each tool page includes methodology, installation commands, I/O formats, and chart reference with preview images.